Hi Everyone,

This is follow-up information/questions to the issue I ran into with the galaxy 
June 2nd, 2014 update.  I hope to receive feedback on how to proceed.


-          Running Galaxy (DB Schema 118) with a MySQL 5.5 back-end

-          When updating galaxy to the june 2nd release, the v120 DB schema has 
referential integrity constraints, which produced errors during the upgrade.

-          Completed two galaxy updates in the past 4 months without 
encountering this before (schema changes included)

In the past, referential integrity in the DB schema was never an issue.  I 
checked backups and the current database to find that the database tables are 
using the MyISAM engine.  MyISAM =  no referential integrity support, no 
I reviewed galaxy's SQLAlchemy templates and determined that 
mysql_engine='InnoDB' isn't set on tables.  This explains why all tables were 
created with the MyISAM engine.  If the mysql_engine is not innodb, SQL Alchemy 
is supposed to drop any referential integrity constraints defined in the 
schema.  What I don't understand is why SQL Alchemy is no longer ignoring the 
referential integrity constraints.

Going forward, can anyone propose how I can salvage the database or continue 
ignoring referential integrity for now?
Assuming that my limited understanding of SQLAlchemy holds water, I was looking 
at fixing the galaxy code base but I need some clarification on the DB schema 
versioning.  Do I edit schema v1 and add the appropriate table args to make 
every table an innodb engine table or do I add a new schema and modify all 
tables to use the innodb engine?  Alternatively, I can use DDL events
def after_create(target, connection, **kw):
    connection.execute("ALTER TABLE %s ENGINE=InnoDB;
   (target.name, target.name))

Thank you for your help.

Iyad Kandalaft

Bioinformatics Application Developer
Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
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